To enable diverse functions and precise regulation,an RNA sequence often folds into complex yet distinct structures in different cellular states.Probing RNA in its native environment is essential to uncovering RNA str...To enable diverse functions and precise regulation,an RNA sequence often folds into complex yet distinct structures in different cellular states.Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts.However,current methods generally require large amounts of input RNA and are challenging for physiologically relevant use.Here,we report smartSHAPE,a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction.Using smartSHAPE,we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation,and provided evidence that RNA conformational changes regulate immune responses.These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems,and also provide a research paradigm for the study of post-transcriptional regulation.展开更多
RNA molecules serve a wide range of functions that are closely linked to their structures.The basic structural units of RNA consist of single-and double-stranded regions.In order to carry out advanced functions such a...RNA molecules serve a wide range of functions that are closely linked to their structures.The basic structural units of RNA consist of single-and double-stranded regions.In order to carry out advanced functions such as catalysis and ligand binding,certain types of RNAs can adopt higher-order structures.The analysis of RNA structures has progressed alongside advancements in structural biology techniques,but it comes with its own set of challenges and corresponding solutions.In this review,we will discuss recent advances in RNA structure analysis techniques,including structural probing methods,X-ray crystallography,nuclear magnetic resonance,cryo-electron microscopy,and small-angle X-ray scattering.Often,a combination of multiple techniques is employed for the integrated analysis of RNA structures.We also survey important RNA structures that have been recently determined using various techniques.展开更多
基金the National Key R&D Program of China(2019YFA0110002 and 2018YFA0107603 to Q.C.Z,and 2020YFA0509100 to X.H.)National Natural Science Foundation of China(Grants No.32125007,91940306,91740204,and 31761163007 to Q.C.Z,and 31725010,31821003,31991174,32030037,82150105 to X.H.)Research Grants Council of the Hong Kong SAR,China Project No.N_CityU110/17 to C.K.K.
文摘To enable diverse functions and precise regulation,an RNA sequence often folds into complex yet distinct structures in different cellular states.Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts.However,current methods generally require large amounts of input RNA and are challenging for physiologically relevant use.Here,we report smartSHAPE,a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction.Using smartSHAPE,we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation,and provided evidence that RNA conformational changes regulate immune responses.These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems,and also provide a research paradigm for the study of post-transcriptional regulation.
基金National Key R&D Program of China(2021YFA1301500,2017YFA0504600,2022YFC2303700,2022YFA1302700,2022YFF1203100)National Natural Science Foundation of China(U1832215,32171191,91940302,32230018 and 32125007)+6 种基金Strategic Priority Research Program of Chinese Academy of Sciences(XDB37010201,XDB0490000)Center for Advanced Interdisciplinary Science and Biomedicine of IHM(QYPY20220019)the Fundamental Research Funds for the Central Universities(WK9100000032 and WK9100000044)Guangdong Science and Technology Department(2022A1515010328,2020B1212060018 and 2020B1212030004)the Postdoctoral Foundation of Tsinghua-Peking Center for Life Sciences[to J.Z.]the Beijing Advanced Innovation Center for Structural Biology[to Q.C.Z.]the Tsinghua-Peking Joint Center for Life Sciences[to Q.C.Z.].
文摘RNA molecules serve a wide range of functions that are closely linked to their structures.The basic structural units of RNA consist of single-and double-stranded regions.In order to carry out advanced functions such as catalysis and ligand binding,certain types of RNAs can adopt higher-order structures.The analysis of RNA structures has progressed alongside advancements in structural biology techniques,but it comes with its own set of challenges and corresponding solutions.In this review,we will discuss recent advances in RNA structure analysis techniques,including structural probing methods,X-ray crystallography,nuclear magnetic resonance,cryo-electron microscopy,and small-angle X-ray scattering.Often,a combination of multiple techniques is employed for the integrated analysis of RNA structures.We also survey important RNA structures that have been recently determined using various techniques.
